A Tale of Two Shepards
by Piper Squeaks
Summary: When "Alex" Shepard was brought back from the dead. He never realized that somewhere in another universe another "Alex" Shepard was having the same bad day. Now the two must save their galaxies AND figure out why the hell they are in the wrong BODIES! A Paragon and a Renegade must live with the consequences of the other's choices, and learn how the other half lives.
1. Alex Shepard Wakes Up

Part 1

"Shepard you have to get up! This facility is under attack!" Shepard! Wake up!"

"Huh. What the… Where am I?" Jonathon Alexander 'Alex' Shepard rose slowly from the operating table. He wobbled on his feet, a wave of dizziness swept over his consciousness as he struggled to regain a semblance of sanity and self-awareness. He stepped once, then twice, then a third time. Each step becoming a little more sound than the last. He rubbed his hands through his hair and tried to focus on the voice that was commanding him to wake up.

"Shepard, your armor and pistol are in the locker in the corner of the room. Get dressed and get moving to the nearest exit." He moved to the locker, and opened it. Inside he found a full set of jet black armor. An N7 logo emblazoned on the chest plate. He grabbed the greaves, the armored boots, the shoulder pieces, and the chest plate. There seemed to be something odd about the chest plate, but he was in too much of a hurry to worry about it at that moment in time.

He slipped off the surgical gown and quickly donned the under armor padded tights and under shirt. He quickly started attaching the armor pieces moving up from his legs to his abdomen, back and arms and finally attached the chest piece. _Huh, weird._ He thought as he inspected the fit of each armor piece. He grabbed the pistol and immediately found something missing. "This pistol is missing something. I'm not sure what it is though." _Huh, my voice is little higher than I'm used to hearing._

"It's missing its thermal clip. I will explain to you about them later. Once you get out of this room we'll find you clips for your pistol. Now get the hell out of there." The Aussie voice cut out

He quickly moved out of the operating room and found himself in another room. On the floor was a small cylindrical object that looked like it might fit in his new sidearm. "Ah-ha. Found one! Uh-umm" _My voice must be going out. It sounds just like…a woman's voice._

Before he could continue to explore the ramifications of that latest thought. Several security mechs entered and began firing at him. "Shepard! Get behind some…"

"Cover! Yes, I am fully aware I need to dodge the incoming projectiles." Alex leaned out of cover and dropped the five mechs with successive head shots. _I have a sexy voice. Why do I have a sexy voice?_ Shepard looked down at his chest and inspected his armor once more. Now that he was really looking at his armor, he realized that it had a distinctly feminine design. _Why am I wearing a set of woman's armor?_ "Why did you make me put on armor designed for a woman?" Shepard asked the disembodied voice.

"Shepard, are you feeling unwell? That armor was specifically fitted for your body?" The voice responded.

"Oh." _Wait. What._ "Wait. What?" Shepard looked once more at her body. _Wait a minute. I haven't had a body this small since I was twelve._ She slipped a hand up to cup one of her chest plate bumps. _I have breasts? Oh shit, I have breasts! Why do I have BREASTS?! _She tentatively reached a hand under the armor plating of her pelvis _I'm A WOMAN! I'VE BEEN TURNED INTO A WOMAN!_

"AAAAAAHHHHHHH! IT'S GONE! WHAT HAVE YOU PEOPLE DONE TO ME! I'M A WOMAN!"

"Yes, of course you're a woman. We brought you back just the same as you were before your… We don't have time for this! You need to get off this station. We can discuss all of your issues once that has been accomplished!"

Shepard grinned maniacally, "I am going to kill all of you! I am going have to kill every single one of you." Shepard picked up the grenade launcher in the next room she came upon and proceeded to relieve some of her rage on the poor security mechs that he saw enter the room from the other side. She stormed through room after room decimating anything that got in her way.

The next door opened onto a bridge-like structure that crossed a wide open chasm. _OK, that's long drop. Wait, that's a real guy crouching over there. Maybe he can give me some answers. _She eyed the uniform, a skin-tight affair in white, and black with gold insignias on it, and some minor pieces of armor plating in key areas. The man himself, was of African descent, with a warrior's build.

"Shepard! Shit must have really hit the fan if Miranda's got you up and moving!" Jacob nodded for her to come over to the railing.

Alex moved quickly over to the bannister and crouched behind the bullet proof glass. "I have no idea what's going on and I need some answers, now!"

"Yeah, answers. Let's take care of the trash and then we can play twenty questions." Jacob popped back up and fired several times hitting a mech in the shoulder and chest.

"You know what, fine!" Shepard jumped up and fired four shots. Each round hitting a different mech dead center in their optics. She paused for a moment. _Damn, that was pretty impressive. I don't think I've ever been that good before. This just keeps getting weirder and weirder._

"OK, you got questions. I can probably guess what the first question might be. It's 'where are we?' right?"

"Huh, that's… Not even remotely close to my first question. My first question is… Why the hell am I a woman?! What, did you guys do, lose my man bits somewhere along the line when you patched me up? What kind of circus is this place? Help me out here, I'm not having a great day!"

"Uh, Shepard, then this will probably come as a shock, but you have always been a woman. You have to remember. The first human SPECTRE was a woman. You. You died, and we brought you back, at considerable expense, I might add. Miranda, the operative in charge of your resurrection can tell you more, but that's the gist anyway."

"OK, let me get this straight. I was a woman. I was born a woman. I died a woman. And I was brought back as a woman. This makes no sense. I'm Jonathon Alexander Shepard, Lieutenant Commander of the Systems Alliance Navy, and a Citadel Council SPECTRE. Oh, and by the way I'm a GUY." Shepard shook her head and hoped that somehow this whole fiasco was just some ridiculous nightmare that she would wake up from at any time.

"Uh, most of that was accurate except for the name… You're Miya Alexandra Shepard, Lieutenant Commander of the Alliance Navy, Council SPECTRE and oh, by the way you're a woman. You know. Broad. Dame. Hot Tchotchke. Any of these words ring a bell."

"Yeah, I'm about a hair's breadth away from ringing your bell… This is crazy! God, I swear, I'm Jonathon Alex…"

"Hello, is anyone there? This is Wilson". The voice overhead announced in a non-Australian accent.

"Wilson, this is Jacob. I have Shepard here. What the hell's going on?" Jacob responded.

"Shepard! She's alive! How the hell… Never mind, I'm in server room B and I've been shot in the leg. One of the security mechs got a lucky shot."

"Wilson, what the hell are you doing in any of the server rooms? You're only allowed access to the bio-wing." Jacob asked with an accusatory tone.

"That doesn't matter right now. We have got to get off this station, as soon as possible. Hurry up, before I bleed out!" The voice then cut out.

"Well, I think we better hurry. Sounds like Wilson is having some issues of his own right now. Rain check on the rest of the questions, Shepard?"

"Yeah, whatever." Shepard followed Jacob through several rooms and corridors. Each room brought a fresh group of mechs to take down. Shepard dropped mech after mech with unerring head shots. _Damn. I'm not even trying and I've racked at least a dozen kills by head shot._

"Shepard, the next room is server room B. Let's see if Wilson can shed any more light on the current events." The two soldiers stepped through the door and found Wilson lying on the floor holding his wounded leg. Shepard looked the room over but found little evidence of a gun fight.

"Shepard, there's some medi-gel in the dispenser on the wall over there." Jacob said as he motioned to the opposite wall. "Grab some so we can patch up this leg wound."

"OK, sure, medi-gel coming up." Shepard stepped over and filled his armor's medi-gel container. _Three doses. Good enough for now I guess. _He stepped back over to Wilson and administered the treatment to the gunshot wound, and then helped Wilson onto his feet. Shepard, noticed that Wilson had his hand on his pistol for a moment, but then he moved it away just as quickly. _Son of a bitch is thinking about offing one of us._

More rooms and mechs later.

OK, Guys the shuttle is just through these doors… Miranda! I thought you were" BANG!

"Dead." Miranda replied as she lowered her pistol. The body dropped to the floor.

"Damnit, Miranda! What are you doing?" Jacob asked as he watched Wilson's body hit the floor.

"My job! Wilson betrayed us all!" Miranda sneered at the dead body looking as if she might kick it at any moment.

"OK, I could tell he was just waiting for an opportunity to shoot me in the back, but you could have captured him. Found out who he worked for. You know, the types of questions that people can answer when they're still alive." Shepard said, as she also watched the body fall to the floor.

"We don't have a lot of time, my employer is eager to speak with you."

"And who the hell is that? I better not find out you guys work for Cerberus or something equally retarded." Shepard said in a huff. Which on the short female SPECTRE was actually quite adorable.

"Let's just get on the shuttle and get out of here." Miranda replied as an inordinately large drop of sweat rolled off the back of her head.

"After you." Shepard motioned for the cat-suited operative to lead on as the other two followed into a waiting shuttle. Shepard paused as she happened to catch her reflection. "Hey guys, what are these glowing scars… I have… I have pi… I Have Pink Hair! Why Do I Have Pink Hair?! WHAT, ON GOD'S GREEN EARTH, DID YOU PEOPLE DO TO ME?!"

End of Part 1

* * *

Part 2

"Shepard you have to get up! This facility is under attack!" Shepard! Wake up!"

"Huh. What the… Where am I?" Miya Alexandra 'Alex' Shepard rose slowly from the operating table. She wobbled on her feet, a wave of dizziness swept over her consciousness as she struggled to regain a semblance of sanity and self-awareness. She stepped once; then twice; then a third time. Each step becoming a little more sound than the last.

"Shepard, your armor and pistol is in the locker in the corner of the room. Get dressed and get moving to the nearest exit." She moved to the locker, and opened it. There sat a complete set of N7 armor. The N7 logo emblazoned on the chest plate. She grabbed the greaves, the armored boots, the shoulder pieces, and the chest plate. There was something odd about the suit, but it wasn't that important right now.

She slipped off her surgical gown, and paused. _What the… I seem to have a rather large appendage. I'm pretty sure that wasn't there before. I'm pretty sure I was a girl yesterday._ She reexamined the armor. _Yep, this is not my armor. I had nice black armor. I'm an infiltrator, I should have black armor. I like black armor! What the hell is this ridiculous shiny steel armor! I can't wear this shit! I'll look like Iron's Man goofy fucking sidekick in this getup! God Damnit!_

He reluctantly put on his armor and adjusted the fit. _Yep, I look like the fucking white Man Of Steel. This is not OK!_ He grabbed the pistol and slammed the locked door closed. _I wake up and I'm a guy. I have bling instead of real armor, and.. A pistol without a heatsink._ This pistol doesn't have a heatsink, how the hell do I use it?" She yelled out into the air.

"There called thermal clips now, and I'm sure you will find some on your way out of this room. Now you have to hurry."

"Yeah, yeah." Shepard waved her hand dismissively. "I have a few questions that need answers before I do anything else that you tell me to. Capiche?"

"What, we don't have a lot of time." The voice continued in her distinctive Aussie accent.

"I'll decide how much time we have. Now first question. Where am I?"

"Lazarus Station. Next."

"That really doesn't tell me shit, you know that right." Alex's voice took on a melodic quality that did not at all mesh with the look of anger on his face.

"You are on a medical space station called Lazarus. You have been on this station for two years while I and my staff did the impossible and brought you back from the dead. Is that better?" The voice asked sarcastically.

"Yes, and knock off that condescending tone before I find you and break my foot off in your haughty Australian ass." Alex muttered as he continued into the next room.

"Ah-ha. Bingo." Shepard grabbed a couple of clips off the floor and slapped one into the pistol's breach. Just in time to see a group of security mechs enter the room from the other exit. "OK, time to lay down the law." He fired at a mech's head, and missed. He fired again at the mech's center of mass and the shot just grazed the target's torso. "Ah! What the fuck is going on? I can't hit the broadside of a cruiser with this stupid piece of shit. This is really pissing me off!"

"Shepard, try your biotics. They might work better in this situation." The voice offered as token of goodwill between the two professionals.

"I'm a fucking spook, not a freak. I don't have biotics!" Shepard announced as he continued firing at the mechs coming through the doors. The first mech finally dropped and he shifted to another position behind cover to keep from getting his head blown off.

"Yes, you do Shepard. I implanted the amp myself a few weeks ago, once I was sure it would not affect your recovery.

"OK… how do I do it?

"Just focus on the mechs and focus what you want done to them." The aussie voice instructed.

"Sounds easy enough. Let's give it a try." Shepard gestured for one of the mechs to rise and an aura of blue energy engulfed his left arm. "Holy shit! I have biotics!" Alex exclaimed as the now helpless mech rose in the air. He gestured again and the mech hit the ground head first and exploded. "Oh, yeah! You mechanical punks are toast!" He continued using the slam attack to demolish the rest of the mechs in the room and continued into the next.

_OK here come another 4 mechs right in a line. Let's see if I can knock them all down at once like some kind of fucked up set of dominoes._ Alex focused and fired a shockwave straight through the ranks and obliterated the bots all at the same time. _Strike! _

"You need to keep moving I don't know how much longer I can keep guiding you." The Aussie announced as Shepard exited into a hallway.

"Look I have a feeling that as long as I keep moving forward I'll be fine. So go do what you gotta do." Shepard moved through the hallway and into a room where he witnessed another scientist type die horribly. _Wow! OK, big ugly mechs have rockets. I should probably file that tidbit away for future use._ The next room seemed to be a bottomless pit with a wide bridge across it. _Who the hell thinks bottomless pits in space stations are good ideas, anyway._

There on the bridge he saw a guy with an above average build and skin-tight uniform crouched behind a railing.

"Shepard! Shit must have really hit the fan if Miranda's got you up and moving!" Jacob nodded for him to come over to railing.

"OK, so who the hell are you?" Shepard asked as he slipped down into cover beside him.

"The name's Jacob Taylor. I imagine you have some questions for me. Let's get rid of the trash and I'll answer them." Jacob said as he looked back over the railing to the line of mechs on the far wall.

"Actually, I think I got the answers I need." Alex popped out of cover, dropped a warp in the middle of mechs and then pulled each one of them off the far wall. "So why don't we play twenty answers and you tell me how well I do? Sound good?"

"Sure, let's see what you know." Jacob motioned for Shepard to continue.

"OK! One, I'm on Lazarus Station. Two, I've been dead for two years. Three, you work for a clandestine organization that thought bringing me back to life was a good idea. That last one alone makes me question your leader's sanity, but we'll burn down that bridge when we come to it. How am I doing so far?" Alex motioned for Jacob to answer his question.

"Not bad. I suppose Miranda told you most of that."

"If you mean the Australian Princess that keeps ordering me around like I'm her personal border collie than yeah you're exactly right."

Jacob chuckled for a moment "Yeah, that sounds like Miranda. So I assume she told you we need to get off this station."

"OK, I'm not one hundred percent clear on the need to abandon this station. We just need to find and kill the SOB that hacked the security mechs; cut off his or her private bits, and reset the mechs so they're friendly again."

"That's Miranda's call, not mine. But there may be more going on than just killer robots."

"Hey, you know what, can I see your pistol for a minute?" Alex grabbed Jacob's pistol before he could answer. He turned and fired several shots at various protrusions on the far wall. "Damn, and I thought my aim sucked because my pistol was shitty."

"What do you mean? It looked like you hit the wall with every shot." Jacob snarked as he waited for Shepard to do whatever he was going to do.

"Oh, you're hilarious! Asshole." Shepard turned the gun over in his hand and was silent for a moment as he contemplated the ramifications of his inaccuracy. _I'm not an infiltrator. I have biotics. I suck with a pistol._ "Jacob, do you happen to have a shotgun on you."

"Yeah, here" Jacob reached behind him and unhooked his eviscerator from the hard point at the small of his back.

"Ah, thanks!" Alex turned and fired several bursts from the shotgun. "Yeah, that feels much better. OK, that answers that question." Shepard turned back to the black agent and motioned for him to lead on.

"Hello, is anyone there? This is Wilson". The voice overhead announced in a non-Australian accent.

"Wilson, this is Jacob. I have Shepard here. What the hell's going on?" Jacob responded.

"Shepard! He's alive! How the hell… Never mind, I'm in server room B and I've been shot in the leg. One of the security mechs got a lucky shot."

"Wilson, what the hell are you doing in any of the server rooms? You're only allowed access to the bio-wing." Jacob asked with an accusatory tone.

"That doesn't matter right now. We have got to get off this station, as soon as possible. Hurry up, before I bleed out!" The voice then cut out.

"Well, you do realize that, if Wilson is doing shit he isn't supposed to be doing, that he's probably the traitor. Right?" Shepard said as the two continued in the direction of the server room and Wilson.

"No, that can't be right. He was one of guys directly responsible for bringing you back." Jacob said in between Shepard's shotgun blasts.

"You know the guy better than I do." Shepard returned to the task of extinguishing the killer robots with a certain reckless abandon. _Damn, who knew being in the line of fire could be so much fucking fun. I love this shotgun!_

The next room they came to was the server room they were looking for. "Now, let's see if Wilson can shed any more light on current events." The two soldiers stepped through the door and found Wilson lying on the floor holding his wounded leg. Shepard looked the room over but found little evidence of a gun fight. Alex then turned his attention to the bald headed idiot lying on the floor. "Huh," He examined the wound "Yeah, that's not good. I don't think you're gonna make it. Jacob, let's go. He's a lost cause."

"Funny, Shepard. The medi-gel dispenser is on the wall over there."

"This man is gonna need a hell of a lot more than medi-gel for that injury! Don't you just see… the look on his face. Damn, I love it when I get somebody to sweat bullets."

"Shepard!" Jacob pointed to the medi-gel dispenser a little more emphatically.

"Yeah, yeah. Don't get your panties in a twist." Shepard walked over and grabbed the three medi-gel doses and then administered a dose on Wilson's leg.

"Yeah, that's the wrong leg, Shepard." Jacob said as he watched the would-be MD treat the patient.

"Whoops, my bad!" Alex gave them a sheepish grin, and then dosed the other leg. "Hey, I never said I was a doctor. He could have gotten the medi-gel himself if he wasn't such a pussy!" Alex turned to Wilson. "Can you walk now? Cause I sure as hell ain't carrying you off this station."

"Yeah, it feels good. Thanks." Wilson then motioned for the two of them to head out of the room.

"Yeah, like I trust either of you two blockheads to not shoot me in the back." Shepard crossed his arms and waited for them to figure out "correct" marching order.

"Look Shepard, if I tell you who we work for will that help you trust us more?"

"Jacob, I don't think now's really the time."

"It's like the Commander said. We aren't going to get very far, if he keeps expecting a shot in the back."

Alex looked at the bickering couple and then said, "Telling me who you work for won't make me trust you two morons any more, but then again telling me couldn't make me trust you any less either, so you may as well get this little confession off your chest." Shepard tapped his foot on floor as he waited for Jacob to spill the big secret.

"Shepard, we work for Cerberus."

"Cerberus, huh. Wow, that's really something. I think I just… can't bring myself to care. Let's just find Miranda and get the hell off this idiotic station.

"Miranda, was over in D wing. That section was swarming with mechs. She's dead by now" Wilson said as he took the lead.

"There's no way some mechs could take out Miranda." Jacob said as he came to Miranda's defense.

"Look is D wing on the way? Cause I'm not looking to take any detours at this point of our escape." Alex asked as he followed the two other men out of the server room.

"Yeah D wing is pretty close to the shuttle bays, which is where we're headed anyway."

"Then, I guess the mystery of Miranda's survival will be solved after all. Now let's double time it; I'm getting hungry." Shepard pushed Jacob and Wilson out the door. After several battles the trio found themselves in front of the entrance to the shuttle bays. As soon as the blast door opened the group came under fire from a large group security mechs.

"Damnit! I need to get in the mix or we'll get gunned down ten feet from the finish line!" Alex stepped out of cover and after a few seconds of intense focus suddenly found himself hurtling through the mech formations. "Woah! Stop!" He violently came to a stop as he crashed headlong into a large shipping crate. "OWWW! Son of a bitch!" He got to his feet and discovered that he had blown through the mechs entirely. The floor was strewn with mech bodies and body parts scattered about as if a bomb had gone off in the middle of the group. "Oh, Snap! I'm going to so enjoy this!"

He found another cluster of mechs on the floor above him and he snap-charged through their ranks, shotgun blazing. Once all of the mechs had been pulverized, he then turned his attention on the crates lying around him. _Damn, now that was shit was fairly fucking awesome if i do say so myself. I think I need some additional practice!_

"Shepard! It's time to go!" Jacob yelled as he watched the former SPECTRE impersonate a human billiard ball.

"Not…" Snap-Charge "Yet…" Shotgun Blast "I'm having…" Snap-Charge "Way too much…" Shotgun Blast "Fucking fun!" Shepard snap-charged again within range of Jacob who immediately grabbed the Commander by the shoulder to stop him.

"You can practice your pinball impersonation skills later. We have to go. Now!" Jacob pulled him along to the final door that would lead the group to a shuttle.

"Hey, where's that Miranda chick…?" Alex asked as he realized he had apparently waltzed through D Wing and never even noticed.

"Miranda. I thought you were…" Bang!

"Dead." Miranda sneered at the falling corpse and kicked him once in the privates for good measure.

"Way to kick a man when he's down… and dead." Shepard gave her a thumbs up and a cocky half-grin.

"Shepard we have to leave now. We don't have a lot of time, my employer is eager to speak with you."

"You mean the Illusory Man. I know you people work for that group of ass-hats known as Cerberus." Shepard shrugged as he stepped past her to look at the shuttle.

"Ah, Jacob. I should've known your conscience would get the better of you. And that's Illusive Man not Illusory.

Shepard turned and looked back at her. "I said Illusory because, like many illusions, I think his shtick is pretty much bull-shit. Now can we leave or are we going to hang out in the shuttle bay until TIM, the 'Tool' Man shows up to pick us up personally." Alex air-quoted the word, tool. He then opened the shuttle door and waited for the two operatives to enter before joining them.

* * *

Author's Notes:

Well now I've gone and done it. I have published my first fan-fiction story. I hope everyone who reads this has a laugh or two even if said laughs are directed at the author. I hope to have chapter two up in a week or two (no promises...).

Below is a small preview of the fun and games that the Shepards will be subjected to in the next chapter:

"And just what is it that you and I know?" Alex asked as he waited for the Illusive Man to finish smoking his cigarette. "Is it the knowledge that smoking causes lung cancer, thereby making you a self-correcting problem?"


	2. Freedom's Progress or Lack Thereof Pt I

AN: Hopefully this chapter somewhat redeems the previous one, as I kind of pushed that one out without really proof-reading it very well. Also regarding the gender pronouns used in this story. The pronouns conform to the physical (not mental) gender of the Shepard in the chapter.

LEGAL DISCLAIMER:

Nope, I don't own Mass Effect. I barely even own the laptop I am writing this fanfic on.

"So, my name is Miya Alexandra Shepard." Alex's steel blue eyes returned to the datapad that was currently displaying a pic and the vital statistics of **this** universe's Shepard. The photo was of a young female Naval officer. Her uniform was crisp and well-fitting. Alex had to admit that she was… cute, beautiful even, in an elfin sort of way. Steel blue eyes gazed back at him. Her eyes seemed to hold a look of mischief, like she knew it was all a big joke, but was just holding in the laughter. Her complexion was creamy almost white and her electric pink pixie cut gave her an air of innocent playfulness that seemed completely incongruent with her reputation. Amongst the rank and file of the Alliance Navy she had earned the nickname…

"Butcher of Torfan? She… I mean **I'm** known as the 'Butcher of Torfan'?" Alex gave an incredulous look to her two shuttle companions, "How the hell does this… girl earn the title 'butcher of'… **anything**." Alex just couldn't wrap her head around it. She shook her head and looked back down at her pic as if it would at any moment provide all of the answers.

Jacob spoke first. "Well, you see… She… I mean you… killed over 150 Batarians single-handedly. And it gets worse. Over 30 of those Batarians had already been captured and were being held for interrogation when she blew up, and shot, or just plain strangled them with her bare hands. And if that wasn't bad enough she… **you** were also brought up on charges for insubordination, striking a superior officer, and war crimes. The charges were all mysteriously dropped, but…" Jacob shrugged and looked over to Miranda to see if there was anything she wanted to add. Miranda just shook her head and looked out of the shuttle's window.

"OK. Moving on. What about my hair? How is it that I have the most 'unique' hair color I've ever seen? I mean glow-in-the-dark pink is kinda out there for an infiltrator isn't it. Was I born with this, or was it some sort of radiological accident? Did I have a school trip to Chernobyl or something?"

Miranda chose that moment to return to the conversation, "No, you definitely were not born with it. I had wondered the same thing as I began piecing you back together, and I discovered that the origin of your bubblegum colored locks was a bizarre side effect to the genetic modification that all N school candidates must receive to become eligible. It was a one in a million occurrence that no one could have predicted. You were, however, born with your height. I actually think you hold the record of galaxy's **shortest** SPECTRE."

Miranda paused for a moment deep in thought then suddenly looked over at Jacob. "What the hell are we going to do? What the hell are we going to tell the Illusive Man… We brought Shepard back but her soul may be from another universe. Oh, and in that universe, Shepard was a man." She shook her head at the impossibility that has now become her life.

Alex looked from one to the other and at that moment decided that if this was the hand she was dealt she would played it to the bitter end. "We tell him that the Lazarus project was a success. Alex Shepard was brought back from the dead." Alex shrugged. "This actually brings me to my last problem. I still can't believe you two work for Cerberus. How did two intelligent and well-adjusted humans like you end up working for that particular brand of insanity?"

"It's a long story." Jacob and Miranda said in stereo.

"Then I'll say this; I'll listen to what the Illusive Man has to say, but I am not going to just fall in line because he asks nicely." Alex said as she went back to studying her counterpart's life history.

KNOWN ASSOCIATES:

LT KAIDEN ALENKO: ALIVE - LOCATION UNKOWN

CHIEF ASHLEY WILLIAMS: KIA - VIRMIRE

LIARA T'SONI: ALIVE - CURRENT LOCATION: ILLUM

TALI'ZORAH VAS NEEMA NAR RAYYA: ALIVE - CURRENTLY LOCATION: THE NEEMA IN THE MIGRANT FLEET

URDONT WREX: KIA - VIRMIRE

FLIGHT LT JEFF MOREAU: ALIVE - CURRENT LOCATION: MINUTEMAN STATION

"I lost Ash here? In my reality, it had been Kaiden. I had needed him to make sure the bomb was properly set. Wait, why was Ashley the one to set up the bomb? Kaiden would have been more qualified to handle the explosive."

"She didn't handle the bomb, she and the Salarian contingent were all lost trying to take down the AA guns."

"What? I sacrificed Ashley AND all of the Salarians?! What the hell was I thinking? Jesus. And can you explain to me why **Wrex** was killed?"

Miranda answered, "It was reported that Wrex was killed by you because he turned traitor. The **rumor** was that Wrex was unhappy with your decision to destroy the facility."

"So you're telling me that I killed Wrex over that stupid genophage 'cure'. Damn it." Alex slumped back in her seat. She continued perusing the datapad for any other relevant data from that might be gleaned from the young infiltrator's career. _It all seems pretty standard. Basic, then N school; fought on Elysium during the Skyillian Blitz. Then, Torfan. What the hell happened on Torfan? _

She closed down the pad and stared at her reflection on the glass of the shuttle's viewport. "I think I can still turn this around. Turn Alex away from the dark path she seemed determined to tread ever since she earned that ridiculous moniker." With that last announcement Alex left her two companions to their thoughts and settled in for some shut-eye.

* * *

Minuteman Station

* * *

Alex stepped off the shuttle and was led into a waiting room where she noticed that her two companions moved to different areas to do whatever it is they do.

"Shepard, if you need any parts of your armor repaired or replaced, you can get them from that armor fabrication unit on the wall. Once you have outfitted yourself, the Illusive Man wants speak with you as soon as possible." Miranda then turned and resumed working on… whatever she had been working on before she spoke with Shepard.

Alex stepped up to the wall unit and activated it. The unit scanned her armor and began fabricating the required armor pieces. It completed its job quickly and Shepard worked to remove the damaged sections and replace them with the new ones. After the armor had been replaced, she stepped down the stairs and entered a medium-sized empty room. Upon standing in the circular depression in the center, two laser scanners scanned her short, slender frame and a hologram projector beamed out a view of a large mostly empty room with only one occupant.

"Illusive Man." The man in an expensive suit nodded. "I thought we'd be doing this face-to-face." Shepard was distinctly unamused with the situation, and the hairs on the back of her neck were standing at parade rest. She crossed her arms, shifted her weight to her left foot, and waited for the man to finish his drink.

"A necessary precaution for people like us. People who know what we know." The Illusive Man took a short drag on the lit cigarette in his hand.

"And what is that we know? Is it that smoking causes lung cancer, atherosclerosis, and stroke; thereby making you a self-correcting problem?"

"Cute. I'm talking about the greatest threat to our brief existence."

"The Reapers." Alex shook her head, as much as she wanted to hate the man in front of her, he had a point.

"Exactly."

"What are the reapers doing that made you decide to bring me back. I mean, hell, that two billion you spent on me could have bought you half of the Alliance and all of the mercs in the Terminus Systems combined. Why spend that kind of money on me?"

"You're more than a soldier. You're a symbol of what mankind can do when necessary. Not to mention, you're one hell of a leader. Humanity needs like you never before."

Alex, channeling her inner renegade was not going to fall for the sweet talk just yet. "What makes you think I'm just gonna fall into bed with Cerberus just because you stroke my ego a little. I need to know what's going on and I need to know now." Alex cocked her head to the side and waited for an answer.

"I didn't think you'd accept any of this on faith. But I'm confident that once you've seen the evidence for yourself your choice will become clear."

"You still haven't answered my question. What is going on?" Alex asked, her arms crossed over her chest.

"To answer your question, the reapers haven't done anything overt, yet. But our colonies in the Traverse are under attack. There have been several instances of whole colonies going silent. When investigated, not a single man, woman or child is ever found." The Illusive Man breathed out a lungful of second hand smoke.

"That doesn't make sense, the reapers want to harvest all of us; not just a handful of colonies on the fringes of the terminus."

"I'd say hundreds of thousands of colonists qualifies as harvesting." The Illusive Man said, and Alex could only nod in reluctant agreement.

"You may not trust me, but I need you to investigate the latest colony to go silent. Freedom's Progress lost contact with the nearest FTL com buoys several hours ago. Go learn what you can, and let me know what you find."

"The Alliance should be the ones investigating this not me or Cerberus."

"The Alliance will get its chance once you're done. I don't want any evidence that may still remain tainted, but don't worry they'll get their chance. Take Lawson and Taylor. They have their orders and understand that you're the lead on this. Good luck, Shepard." At the push of a virtual button the hologram of the Illusive Man disappeared.

"I hate that guy." Alex muttered to herself as she climbed the stairs back to the two waiting Cerberus operatives.

"You two know your orders. Let's just get this over with." Alex led the two back to the shuttle.

* * *

Freedom's Progress

* * *

The trio stepped out of the shuttle and Jacob doled out the group's weapons and handfuls of thermal clips. "Let's keep this simple. We look for clues and try to assist anyone that may have somehow survived the attack." She looked down at the sniper rifle in her hands. The weapon was massive. "Did I really carry this thing around on missions, it's almost as long as I am tall."

"Longer actually by zero point four centimeters. You called it the Black Widow. This one is a copy based on vids of your exploits during your mission to bring down Saren." Jacob wielded a shotgun from his back and Miranda held her machine pistol. Shepard could only nod and hope that somehow her body would know what to do when the MA rounds started flying.

"OK, let's do this by the numbers. Standard stagger formation we clear each building, mark and move on. That clear to everyone." The two subordinates nodded their heads as they moved away from the shuttle and into the first prefab. The first building seemed to have food left from whenever the colonists were abducted.

"What the...? Did they all just get up and leave?" The room looked like everyone had just gotten up and left. "There are no signs of any fighting." Alex looked around for any signs of a gun battle. "Not even any bullet holes. Does this make any sense to either of you? Were all the previous colonies like this?"

"Yes the previous abductions just as few clues as this one. I think it seems pretty obvious that whatever we're dealing with might have a way to incapacitate people from a distance." Miranda began scanning the cups and plates for any genetic residue that might identify who lived in this particular prefab.

"Miranda, don't worry about identifications just yet I think we need to move fast to find out anything of use. We should leave the ID'ing to the Alliance." Alex motioned for the team to continue to the exit.

"Contact! Two drones and two light security mechs." Jacob was the first one out the door and the first to notice the enemy mechs. He threw a pull on one of the two LOKI mechs and Miranda dropped a warp on the other. The warp detonated nicely as the two mass effect fields overlapped. The two mechs were completely dismantled by the Cerberus biotics.

Alex brought the large sniper rifle to bear on one of the drones and fired. The shot gazed the flying machine but did little real damage. "Damnit!" She scoped the drone again and fired. The follow-up shot missed completely.

"Shepard I think you're trying too hard! Just relax and let your body do what it's trained to do." Miranda fired on a new target. Two more mechs had entered into the combat zone.

Alex closed her eyes and emptied her mind of any stray thoughts. She opened them again and simply let her muscle memory take over. Her finger pulled the trigger twice in rapid succession. Both drones exploded. She turned and spotted a rather large four legged mech running toward the group. She breathed in once and with a quick motion scoped and fired the rifle all between two heartbeats. The heavy mass accelerator round nailed the dog-like mech in an optic and it dropped like a sack of potatoes.

"OK. Let's move on people. I have a feeling someone's still here. Either that or our mysterious colony-knappers decided to leave some nasty parting gifts." Both Jacob and Miranda nodded and took positions on either side of her as she activated the door mechanism.

Alex stepped through the door first and immediately noticed a group of Quarians. They seemed to be arguing about what to do with the new arrivals.

"I said I'm in charge Prazza. Now stand down while I try to figure out what is going on." The lead quarian was wearing a very familiar enviro-suit. The female quarian looked over the three and immediately recognized the Cerberus logos on the uniforms of two of the three that had entered the room. But it was the identity of the third member of the trio that had her the most perplexed. "Shepard, is that you?"

"Those are Cerberus operatives!" The one known as Prazza announced as he and squad brought their weapons to bear once more.

"Weapons down, Prazza! Shepard is that really you?" Tali stepped a little closer to her former captain.

"Tali! God, it's good to hear your voice." Alex dropped her rifle to her side and motioned for Miranda and Jacob to do the same. "Yeah, it's me. How have you been?"

"What is your old commander doing working for Cerberus?" Prazza asked as he nervously twitched his trigger finger.

"I don't know."Tali looked back to Shepard expectantly.

"I can prove it's me, Tali. Do you remember that Geth data that I gave you? Did it help you on your pilgrimage?"

Tali eyed her suspiciously, her luminescent eyes narrowing "What Geth data? You never gave me any... Wait a minute. Are you saying you discovered data on the Geth that you never shared with me!"

"Uh, of course not, Tali."_Oh crap! Don't tell me I never managed to find that Geth data cache either! What the hell was I doing when I went after Saren? _Alex had to backpedal quickly. "I would never do anything like that. I was... verifying that it was really you that's all."

Miranda and Jacob just held their heads and sighed.

"Uh huh. Next you'll tell me that leaving me in engineering all those times you went out on missions was just for my own safety!" She stopped and thought for a second. "Wait, any Geth data at all would have made a much better pilgrimage gift than what I ended up with. I had to settle for an old rusty used freighter. I was so embarrassed I couldn't even look at my father for over two weeks!" The young engineer was growing more angry by the second.

"So Tali do you know what is going on here by any chance?" Shepard could see the young quarian becoming more and more agitated and she needed to move away from the current topic as quickly as she could.

Recognizing the diversion tactic for what it was Tali decided to let the matter drop for the moment and answered, "Yes, a young quarian by the name of Veetor was using his pilgrimage to help this colony upgrade their communications arrays. He liked the idea of working with a smaller settlement as he was always nervous around large crowds."

Prazza then spoke up, "What she means to say is that Veetor was unstable. Combine that with damage to his suit's CO2 scrubbers and an open air infection from a suit puncture, and he's probably delirious."

Tali interrupted her subordinate and said, "He probably re-programmed the mechs to attack anything that is not him."

"We should work together to get to him." Alex internally sighed as he seemed to have successfully diverted her attention back to the problem at hand.

"Agreed, we'll need two teams to get past the drones anyway."

"Now, we're working with Cerberus!" Prazza interjected becoming incensed at the idea of working with the enemy.

"No Prazza, you work for me! You can't do that, you can go wait on the ship!" Tali turned back to Shepard. "And don't think that just because we have to save Veetor that you are completely forgiven. When this is done, you and I are going to have words. Understood?"

Alex nodded, "Be careful Tali, as much as I'm not looking forward to your words; I do want to hear them."

"You too, Shepard. And as much as I may be angry right now it's still good to have you back." She turned and followed her team out the door.

Shepard turned to her team. "That went... did Miya not do **anything** the same way I did!"

"Well, in your, her, defense, Saren and his Geth seemed to be attacking everywhere at once. I remember when I was with the Corsairs, the Alliance was having a hell of a time even keeping up with the onslaught. She, you, were probably doing everything you could to do to stay even one step behind Saren. All other problems had to take a backseat." Jacob again took point as team Shepard moved down a flight of stairs. Shepard nodded in recognition of the difference between her realities. _If that's true then I must have had it much easier. In my reality the Geth never attacked more than a handful of colonies. _

At the bottom of the stairs the group was ambushed by seven flying drones. The trio scrambled behind whatever cover they could find and Alex set up her rifle and immediately began calling shots. The two biotics interspersed gun shots with biotic warps, pulls, and throws whenever the opportunities arose. Alex found herself trusting her body more and more. The Black Widow became an extension of her arms. Every successive shot she fired was more accurate than the last. Her time perception as she scoped her targets became more and more dilated. Her heart rate and breathing slowed dramatically, and her ability to track and lead moving targets increased exponentially.

"Shepard, Prazza ran ahead trying to get to Veetor before you. I need you to move your team into position in front of that loading gate and get ready." Tali announced over the radio as she got into position to hack into the gate controls.

"Understood, as soon as we're in position I'll let you know." Alex motioned for Miranda and Jacob to take up positions to the left and right of the gate and then slipped behind some cover directly in front. "OK, Tali we're ready."

"I'm opening the gate now." Tali fiddled with her omni-tool and the gate slid open.

Once the gate was open Shepard's team sprinted in just in time to watch a large ogre of a security mech slaughter Prazza and his squad. Alex turned away momentarily, disgust at the needless loss of life roiling in her stomach.

"Shepard, this thing is gonna be a bitch to take out. What do you want us to do?" Miranda asked as the three grabbed some cover around several crates that littered the loading dock.

"You two stay down here and keep it distracted. I'm gonna find some higher ground and then we'll pincer the damn thing." Shepard keyed the cloaking function on her omni-tool and scrambled up to an open window on the outskirts of the impromptu battleground. The YMIR mech stalked the two biotics as each of them took opportunities to overwhelm its shield and compromise its armor.

"Hey! Over here you big lug!" Shepard yelled out the window distracting the mech from stalking around Jacob's crate. She cloaked once more, then waited for the tell-tale crash of a shattered shield. Miranda's third overload zapped the last of the shield's strength and in one swift move, Alex slid back to the rear of the room in which she was sitting and from a half crouch, half stance scoped the mech's head and fired the thermal clip's full capacity. The last shot exited the barrel before the first even hit the target. Three massive shots to the head and it popped like a balloon.

"Jacob, Shepard stay down these things blow just like the others when their heads…" BOOM! "Are hit." Miranda and Jacob picked themselves up off the ground as Shepard joined them and the three found Tali once more. She was administering to the few quarians that were left.

"Tali, are you OK?" He reached down placed a comforting hand on Tali's shoulder.

"We do most of the ground fighting and does she ask us if we're all right? No." Miranda muttered unhappily under her breath. Alex looked back at her with a scowl. But said nothing.

"Yeah, I'm good, but you better go find Veetor before we have any more surprises." Tali turned back to her wounded compatriot, and continued working on her wounds and suit punctures.

"Right," Alex took the lead as the three Cerberus agents entered the security building. They found Veetor at the rear of the room working the vid wall in front of him.

"Seekers must not find me. They'll come back and take me as well…" Alex couldn't get a word in edgewise through Veetor's semi-coherent rambling. Quickly becoming exasperated she activated the overload and the vid wall goes blank, causing Veetor to stop and turn around.

"You escaped the monsters. They didn't find you. How did the swarms not find you?" Veetor is understandably confused regarding the trio's appearance.

"We weren't here when the monsters came, Veetor. You have to tell us what happened." Shepard said using a conciliatory voice.

"You didn't see them. The monsters came and took everyone away." Veetor activated his omni-tool's vid playback and routed the signal to the vid wall. The screens come alive with the horrors of a mass abduction.

"I think those are… Collectors." Miranda spoke up as she watched the vid of several insect-like bipeds unceremoniously dump several humans into boxes that looked suspiciously like floating coffins.

"What the hell are the Collectors?" Alex asked she watched the vids, a look of revulsion on her face.

"Collectors are an alien species that seem to live beyond the Omega-4 relay. But only a small handful of people have ever seen one, and even less have had direct communication with them. They usually work through intermediaries, like slavers and mercenaries." Jacob said as he looked over to Alex and shrugged his shoulders. "If the collectors are acting against human colonies directly, they could be working for the reapers."

"Let's grab the Quarian and head back to base; the Illusive Man is going to want to question him to find out if he knows any more about the colonists' abductions."

Miranda said as she reached for Veetor's right arm.

"He's sick. He needs medical attention not an interrogation! You are free to take his omni-tool data, but please let me take him back to the flotilla. I will make sure that any additional information he has is forwarded to you as soon as I can." Tali walked up to the short former SPECTRE, eyes imploring.

"Tali's right, Veetor needs medical care. Miranda, grab his omni-tool." Alex said as she moved to stand closer to Tali. "Wow, Tali. You're tall. I'm like… chin height to you." Tali only tilts her head quizzically toward her in response.

"Yes, Commander." Miranda replied as she began copying the data from Veetor's omni-tool to hers.

After the copy process was completed. Alex said, "OK, you two head back to the shuttle. Tali and I need to talk."

"But Commander, we should stay with you in case…" Miranda began, before she got cut off by Shepard.

"No, go to the shuttle." Alex turned back to Tali, a clear sign of dismissal. "Tali, you wanted to have words, remember?"

Tali helped Veetor out of the room and the two friends waited until the other Cerberus Agents had left as well. "Were you telling me that you withheld data that might have been useful in fighting the Geth? Because even though we were never very close, I always thought you were my friend." Tali looked more nervous than angry at that moment and she began wringing her hands cutely.

"Tali, what I'm about to tell you is going to probably be so unbelievable that it will border on the insane. But you have my word it will all be the truth." Alex paused for a moment before pushing ahead with her tale. "I may look like Miya "Alex" Shepard, Alliance Commander, and Council SPECTRE, but I'm not. My name is Jonathon Alexander Shepard, and in the universe I come from, you and I were… are good friends. I don't know how but I got… put in the body of the person you know as Miya. I know that sounds completely crazy, but it's the truth."

Tali looked at him, disbelief clear in her luminescent eyes. "You're telling me that your souls got swapped?"

"I don't know if we got swapped, or if I'm just in her body and she's off in heaven…" _Or, given her track record, hell._

"What's a heaven?" Tali asked her head inclining slightly.

"That's not important. What is important is that you and I were friends, and as long as I'm here I want to be friends again." Alex laid a hand on Tali's to stop the Quarian's hand wringing.

Tali looked down at the hand on hers still coming to terms with the idea that the woman in front of her had someone else's soul. Someone that she supposedly knew very well. OK, not her, but another version of her somewhere in another galaxy, in another universe. "Let's say for argument's sake I believe you. Did I say something to you, something personal that only friends would have shared? Because I didn't talk to Shep…Miya very much during my time on the Normandy. Oh, this is so crazy…"

"Yes! You did, we did. We talked a lot about your pilgrimage, your life in the flotilla, and a lot about your family especially about your father Rael."

"Okay, then tell me something about my father." Tali's hands visibly relaxed and her manner became less guarded.

"He was an admiral, and one of the five members of the Admiralty Board. He and your Aunt Raan raised you after your mother passed, though you told me that it was more your aunt than your father as he was always emotionally distant…"

"That's enough." Tali said sounding happier than Shepard had heard her since the he first saw her in the prefab. "How do you know all that?"

"I told you Tali, you and I are friends and I enjoyed the time we spent together between missions immensely."

Tali looked down. "Shep… Miya and I never spent much time together during our mission to stop Saren. She was always too busy to stop and listen to me for very long" She paused to catch her breath. "I would like to get to know you like you seem to know me."

"Then come with us. The mission I have now is just as important, maybe even moreso, as our fight against Saren and the Geth."

"I can't I have a mission of my own. I have to finish it before I can think of going anywhere else."

"Can you tell me about it. Do you need any assistance?" Alex was suddenly worried for Tali.

"It's in Geth space. But I have good people working with me, and I'll be careful. When it's over though I think I would like joining your crew again. If you still need my help that is."

"Deal." Shepard took Tali's hand in hers and gave it a solid shake. "Now go get your people out of here."

The two exchanged extranet addresses, and Alex returned to the Cerberus shuttle after seeing Tali to her ship where Veetor and the other quarians were waiting for her. "Let's get out of here." Miranda and Jacob nodded and the three boarded their shuttle and departed without another word.

* * *

Minuteman Station

* * *

"So the mission went well, and now we know the Collectors are involved in the abductions." The Illusive Man sat in here in his chair framed by the young star in the picture window behind him.

"My female intuition is telling me you knew that already."

"I had my suspicions, but I still needed proof. As for the quarians, Miranda's report spoke highly of your old crewmate Tali'Zorah."

"She's a talented engineer any ship would be lucky to have her on its crew."

"Speaking of crew, I compiled a list of some truly outstanding individuals, I forwarded you dossiers on the best of them."

"I had a crew, a damn good one at that. Why can't I have them?"

"I'm afraid that's not possible. Most of them are beyond even my ability to recruit. Lt. Alenko is working on a secret Alliance mission. The last I heard of his whereabouts was when he was on the Citadel working with Councilor Anderson. And according to our intel Dr. T'Soni is working with the Shadow Broker. You can understand my reluctance to have a potential security leak among your staff."

"Fine. So they're unavailable, I get it. Send me the dossiers, but I make the final decisions on my staff."

The Illusive Man nodded and sent her the requested data. "One last thing, I have a pilot that you might like. I hear he's one of the best. I brought you back, time for you to do what you do best." The hologram flickered and the Illusive Man was gone.

Standing behind the former Commander was none other than Flight Lt. Jeff Moreau, his trademark hat somewhat askew. "Damn, it really is like a looking at a ghost."

Alex turned quickly and smiled "Joker! Damn you're a sight for sore eyes."

"Good to see you too. Though I figured you'd probably punch me in the face if you ever saw me again, you know for getting you spaced. I mean your last words to me were. 'If you don't get out of that chair, I'll shoot you myself'."

"Yeah, that sounds like me." Alex internally cringed at the thought of her spiritual counterpart threatening violent death on one of her own crew.

"So, I just heard about it last night." Joker pointed to the large picture window and the two watched as the shape of the new SR class frigate became visible through the darkness of the station's dock.

"I guess we'll have to give her a name." The two look on fondly at their new home.

AN: OK that was… Yeah pretty much canon-balled this chapter. The Freedom's Progress mission was IMHO a good way to get back into the swing of ME. The next chapter will focus on Miya's "play-thru" of Freedom's Progress and the ramifications of some Jonathon's choices as a Paragon. I can tell you now she will not be amused.

Note: She hardly ever IS amused.


End file.
